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From: <pi...@pc...> - 2005-03-04 15:07:59
|
There may be other uses of RNAFeature but the plugins I run use RNA feature for mRNA features either predicted from an assembly of transcript sequences or an mRNA sequence obtained from GenBank. Currently, RNAType and RNAFeature have quite different attributes and seem to be intended for different uses although it may be that they can be consolidated as they are both views of RNAFeature. Quoting Ed Robinson <ero...@ug...>: > What do you use RNA feature for as opposed to RNA type? > > ---- Original message ---- > >Date: Fri, 4 Mar 2005 09:33:19 -0500 > >From: pi...@pc... > >Subject: Re: [Gusdev-gusdev] Trash Tables > >To: Ed Robinson <ero...@ug...> > >Cc: gus...@li... > > > >We definitely use RNAFeature but I am not so sure about > ExonLocation. These are > >issues that should be raised in the schema discussions > because we may want to > >consolidate the views. > > > > Debbie > > > > > > Quoting Ed Robinson <ero...@ug...>: > > > >> We've stumbled upon a couple tables/views which seem > >> redundant. Is anyone using these? > >> > >> Dots.ExonLocation - is completely subsumed by the fields in > >> dots.nalocation. > >> > >> Dots.RNAType, vs Dots.RNAFeature, these tables seem to belong > >> to one concept of a RNAFeature, is anyone using RNAFeature? > >> We want to use RNAType. > >> > >> All and any feedback would be appreciated. > >> > >> -Ed > >> > >> > >> > >> ----------------- > >> Ed Robinson > >> Center for Tropical and Emerging Global Diseases > >> University of Georgia, Athens, GA 30602 > >> ero...@ug.../(706)542.1447/254.8883 > >> > >> > >> ------------------------------------------------------- > >> SF email is sponsored by - The IT Product Guide > >> Read honest & candid reviews on hundreds of IT Products > from real users. > >> Discover which products truly live up to the hype. Start > reading now. > >> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > >> _______________________________________________ > >> Gusdev-gusdev mailing list > >> Gus...@li... > >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > >> > > > > > ----------------- > Ed Robinson > Center for Tropical and Emerging Global Diseases > University of Georgia, Athens, GA 30602 > ero...@ug.../(706)542.1447/254.8883 > |
|
From: Ed R. <ero...@ug...> - 2005-03-04 14:36:37
|
What do you use RNA feature for as opposed to RNA type? ---- Original message ---- >Date: Fri, 4 Mar 2005 09:33:19 -0500 >From: pi...@pc... >Subject: Re: [Gusdev-gusdev] Trash Tables >To: Ed Robinson <ero...@ug...> >Cc: gus...@li... > >We definitely use RNAFeature but I am not so sure about ExonLocation. These are >issues that should be raised in the schema discussions because we may want to >consolidate the views. > > Debbie > > > Quoting Ed Robinson <ero...@ug...>: > >> We've stumbled upon a couple tables/views which seem >> redundant. Is anyone using these? >> >> Dots.ExonLocation - is completely subsumed by the fields in >> dots.nalocation. >> >> Dots.RNAType, vs Dots.RNAFeature, these tables seem to belong >> to one concept of a RNAFeature, is anyone using RNAFeature? >> We want to use RNAType. >> >> All and any feedback would be appreciated. >> >> -Ed >> >> >> >> ----------------- >> Ed Robinson >> Center for Tropical and Emerging Global Diseases >> University of Georgia, Athens, GA 30602 >> ero...@ug.../(706)542.1447/254.8883 >> >> >> ------------------------------------------------------- >> SF email is sponsored by - The IT Product Guide >> Read honest & candid reviews on hundreds of IT Products from real users. >> Discover which products truly live up to the hype. Start reading now. >> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > ----------------- Ed Robinson Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 ero...@ug.../(706)542.1447/254.8883 |
|
From: <pi...@pc...> - 2005-03-04 14:33:24
|
We definitely use RNAFeature but I am not so sure about ExonLocation. These are
issues that should be raised in the schema discussions because we may want to
consolidate the views.
Debbie
Quoting Ed Robinson <ero...@ug...>:
> We've stumbled upon a couple tables/views which seem
> redundant. Is anyone using these?
>
> Dots.ExonLocation - is completely subsumed by the fields in
> dots.nalocation.
>
> Dots.RNAType, vs Dots.RNAFeature, these tables seem to belong
> to one concept of a RNAFeature, is anyone using RNAFeature?
> We want to use RNAType.
>
> All and any feedback would be appreciated.
>
> -Ed
>
>
>
> -----------------
> Ed Robinson
> Center for Tropical and Emerging Global Diseases
> University of Georgia, Athens, GA 30602
> ero...@ug.../(706)542.1447/254.8883
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Sucheta T. <su...@vb...> - 2005-03-04 13:59:51
|
You are right. I vote for nalocation and rnatype too.. Sucheta > We've stumbled upon a couple tables/views which seem > redundant. Is anyone using these? > > Dots.ExonLocation - is completely subsumed by the fields in > dots.nalocation. > > Dots.RNAType, vs Dots.RNAFeature, these tables seem to belong > to one concept of a RNAFeature, is anyone using RNAFeature? > We want to use RNAType. > > All and any feedback would be appreciated. > > -Ed > > > > ----------------- > Ed Robinson > Center for Tropical and Emerging Global Diseases > University of Georgia, Athens, GA 30602 > ero...@ug.../(706)542.1447/254.8883 > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide > Read honest & candid reviews on hundreds of IT Products from real users. > Discover which products truly live up to the hype. Start reading now. > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > -- Sucheta Tripathy Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 |
|
From: Ed R. <ero...@ug...> - 2005-03-03 19:46:58
|
We've stumbled upon a couple tables/views which seem redundant. Is anyone using these? Dots.ExonLocation - is completely subsumed by the fields in dots.nalocation. Dots.RNAType, vs Dots.RNAFeature, these tables seem to belong to one concept of a RNAFeature, is anyone using RNAFeature? We want to use RNAType. All and any feedback would be appreciated. -Ed ----------------- Ed Robinson Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 ero...@ug.../(706)542.1447/254.8883 |
|
From: Alberto D. <da...@io...> - 2005-03-02 21:19:18
|
Hi Steve, If I may, I would like to have a look in your "loading assembly" plugin... maybe we could adapt it to work with CAP3 and the postgres install. Thanks, Alberto On Sun, 2005-02-27 at 08:50 -0500, Steve Fischer wrote: > Jeetendra- > > sorry, i was on vacation. (i am posting this to gusdev) > > unfortunately, the plugin we use for that was written a while ago, > specifically for our DoTS project. It calls CAP4 to do the assembling, > and then writes the assemblies into the db. A better design would have > separated the two steps (assembling and loading). > > If you'd like i could send you that plugin. Perhaps you could use it > as a starting point. We'd be interested in a plugin that loaded > assemblies, because we'll be retiring this plugin within the year probably. > > steve > > Jeetendra Soneja wrote: > > > > > Hi Steve > > > > I have a set of assembly sequences that I would like to load into GUS. > > GUS has Assembly and AssemblySequence tables for this. > > > > However, I couldn't find a plugin which does this. > > > > What do you think is the best way to load such data into GUS ? > > > > Thanks a lot, > > Jeetendra. |
|
From: <pa...@pa...> - 2005-03-02 19:47:11
|
<p>Hi all,</p><p /><p>is there a new LoadBlastSimFast "in the market" <br />with new options:</p><p>- queryIdColumnName</p><p>- subjectIdColumnName</p><p /><p>as Arnaud and Steve were discussing back i= n the list archives? (<a href=3D"http://sourceforge.net/mailarchive/message.php?msg_id=3D9740308">= http://sourceforge.net/mailarchive/message.php?msg_id=3D9740308</a>)</p><= p /><p>Thanks,</p><p /><p>Pablo</p><p /><p>< Hi Poliana, < < Just as a first cut, make sure you have generated your perl GUS objects < recently. Make sure the file < < {$GUS_HOME}/lib/perl/GUS/Model/DoTS/ExternalAASequence.pm < < exists. < < Also, I saw your other comment about the similarity fil= e having the < sequences source ids instead of <br />GUS IDs. That is no= t a problem if, in the < <br />DoTS.ExternalAASequence table, those sequence source ids show up in the < 'name' attribute. Unless you consciously loaded them that way <br />though, < that may not be the case, and you should probably <br />substitute the ids with < GUS Ids in the blast file (I find I <br />have to do that a lot when running < this plugin.) < < However, even if the sequence source ids are not in the 'name' attribute < of that table, I don't think that is the reason for <br />the error you mention < when running the plugin. < < Dave < < < < < On Wed, 2 Mar 2005, Poliana Mateus wrote: < <br /></p> |
|
From: Sucheta T. <su...@vb...> - 2005-03-02 18:40:49
|
Hi Poliana, If you try to load the way it is, it may not do the job. You need to substitute NP_148637 by plain numbers, because this is going to be the subject_id which needs be a number. The best way will be substitute these values with gi numbers. And these values need to be there in the subject_table, that you are going to supply while uploading this data. Sucheta At 02:58 PM 3/2/2005 -0300, you wrote: >Hi Sucheta, > >I found in the list a message its on the LoadBlastSimFast. > >Your archive is: >-------------------------------------------------------------------------------------------------- > > 436644 (242 subjects) >Sum: NP_148637.1:::149:408:927749:1330362:1:1905:108:182:0:-2 >HSP1: NP_148637.1:108:182:1905:::149:408:927749:1330362:0:-2 >Sum: NP_558777.1:::181:440:927740:1330359:1:1808:103:163:0:-2 >--------------------------------------------------------------------------------------------------- > >You it substituted values as "NP_148637.1" for GusID's? Or it inserted >thus exactly in the database (dots.similarity and >dots.similarityspan)? > >Poliana |
|
From: Dave B. <db...@pc...> - 2005-03-02 18:32:28
|
Hi Poliana,
Just as a first cut, make sure you have generated your perl GUS objects
recently. Make sure the file
{$GUS_HOME}/lib/perl/GUS/Model/DoTS/ExternalAASequence.pm
exists.
Also, I saw your other comment about the similarity file having the
sequences source ids instead of GUS IDs. That is not a problem if, in the
DoTS.ExternalAASequence table, those sequence source ids show up in the
'name' attribute. Unless you consciously loaded them that way though,
that may not be the case, and you should probably substitute the ids with
GUS Ids in the blast file (I find I have to do that a lot when running
this plugin.)
However, even if the sequence source ids are not in the 'name' attribute
of that table, I don't think that is the reason for the error you mention
when running the plugin.
Dave
On Wed, 2 Mar 2005, Poliana Mateus wrote:
> Hello All,
>
> I'm trying to run the LoadBlastSimFast...
>
> And I get the following error message:
>
> ----------------------------------------------------------------------------------------------------------------------
> [poliana@phytomonas Plugin]$ ga GUS::Common::Plugin::LoadBlastSimFast
> --file=/usr/local/GUS/Blast/scripts/8saida.out
> --queryTable=DoTS::ExternalAASequence
> --subjectTable="DoTS::ExternalAASequence" --commit
>
> Wed Mar 2 15:07:11 2005 ARGS algoinvo 1
> Wed Mar 2 15:07:11 2005 ARGS batchSize 1000
> Wed Mar 2 15:07:11 2005 ARGS comment
> Wed Mar 2 15:07:11 2005 ARGS commit 1
> Wed Mar 2 15:07:11 2005 ARGS debug
> Wed Mar 2 15:07:11 2005 ARGS file
> /usr/local/GUS/Blast/scripts/8saida.out
> Wed Mar 2 15:07:11 2005 ARGS group
> Wed Mar 2 15:07:11 2005 ARGS gusconfigfile
> /usr/local/GUS/gus_home/.gus.properties
> Wed Mar 2 15:07:11 2005 ARGS hspMatchLength
> Wed Mar 2 15:07:11 2005 ARGS hspPctIdent
> Wed Mar 2 15:07:11 2005 ARGS hspPvalue
> Wed Mar 2 15:07:11 2005 ARGS hspsLimit
> Wed Mar 2 15:07:11 2005 ARGS maxSubjects
> Wed Mar 2 15:07:11 2005 ARGS minSubjects
> Wed Mar 2 15:07:11 2005 ARGS noHSPs 0
> Wed Mar 2 15:07:11 2005 ARGS project
> Wed Mar 2 15:07:11 2005 ARGS queryTable DoTS::ExternalAASequence
> Wed Mar 2 15:07:11 2005 ARGS restartAlgInvs
> Wed Mar 2 15:07:11 2005 ARGS sqlVerbose
> Wed Mar 2 15:07:11 2005 ARGS subjectMatchLength
> Wed Mar 2 15:07:11 2005 ARGS subjectPctIdent
> Wed Mar 2 15:07:11 2005 ARGS subjectPvalue
> Wed Mar 2 15:07:11 2005 ARGS subjectTable DoTS::ExternalAASequence
> Wed Mar 2 15:07:11 2005 ARGS subjectsLimit
> Wed Mar 2 15:07:11 2005 ARGS testnumber
> Wed Mar 2 15:07:11 2005 ARGS usage
> Wed Mar 2 15:07:11 2005 ARGS user
> Wed Mar 2 15:07:11 2005 ARGS verbose
> Wed Mar 2 15:07:11 2005 ARGS veryVerbose
> Wed Mar 2 15:07:11 2005 COMMIT commit on
>
> Can't locate object method "new" via package
> "DoTS::ExternalAASequence" (perhaps you forgot to load
> "DoTS::ExternalAASequence"?) at
> /usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadBlastSimFast.pm
> line 381, <GEN0> line 563.
>
> ---------------------------------------------------------------------------------------------------------------------------------
>
> My table DoTS::ExternalAASequence already was loaded.
> ??
>
> Poliana
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Poliana M. <pol...@gm...> - 2005-03-02 18:17:14
|
Hello All, I'm trying to run the LoadBlastSimFast... And I get the following error message: ---------------------------------------------------------------------------------------------------------------------- [poliana@phytomonas Plugin]$ ga GUS::Common::Plugin::LoadBlastSimFast --file=/usr/local/GUS/Blast/scripts/8saida.out --queryTable=DoTS::ExternalAASequence --subjectTable="DoTS::ExternalAASequence" --commit Wed Mar 2 15:07:11 2005 ARGS algoinvo 1 Wed Mar 2 15:07:11 2005 ARGS batchSize 1000 Wed Mar 2 15:07:11 2005 ARGS comment Wed Mar 2 15:07:11 2005 ARGS commit 1 Wed Mar 2 15:07:11 2005 ARGS debug Wed Mar 2 15:07:11 2005 ARGS file /usr/local/GUS/Blast/scripts/8saida.out Wed Mar 2 15:07:11 2005 ARGS group Wed Mar 2 15:07:11 2005 ARGS gusconfigfile /usr/local/GUS/gus_home/.gus.properties Wed Mar 2 15:07:11 2005 ARGS hspMatchLength Wed Mar 2 15:07:11 2005 ARGS hspPctIdent Wed Mar 2 15:07:11 2005 ARGS hspPvalue Wed Mar 2 15:07:11 2005 ARGS hspsLimit Wed Mar 2 15:07:11 2005 ARGS maxSubjects Wed Mar 2 15:07:11 2005 ARGS minSubjects Wed Mar 2 15:07:11 2005 ARGS noHSPs 0 Wed Mar 2 15:07:11 2005 ARGS project Wed Mar 2 15:07:11 2005 ARGS queryTable DoTS::ExternalAASequence Wed Mar 2 15:07:11 2005 ARGS restartAlgInvs Wed Mar 2 15:07:11 2005 ARGS sqlVerbose Wed Mar 2 15:07:11 2005 ARGS subjectMatchLength Wed Mar 2 15:07:11 2005 ARGS subjectPctIdent Wed Mar 2 15:07:11 2005 ARGS subjectPvalue Wed Mar 2 15:07:11 2005 ARGS subjectTable DoTS::ExternalAASequence Wed Mar 2 15:07:11 2005 ARGS subjectsLimit Wed Mar 2 15:07:11 2005 ARGS testnumber Wed Mar 2 15:07:11 2005 ARGS usage Wed Mar 2 15:07:11 2005 ARGS user Wed Mar 2 15:07:11 2005 ARGS verbose Wed Mar 2 15:07:11 2005 ARGS veryVerbose Wed Mar 2 15:07:11 2005 COMMIT commit on Can't locate object method "new" via package "DoTS::ExternalAASequence" (perhaps you forgot to load "DoTS::ExternalAASequence"?) at /usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadBlastSimFast.pm line 381, <GEN0> line 563. --------------------------------------------------------------------------------------------------------------------------------- My table DoTS::ExternalAASequence already was loaded. ?? Poliana |
|
From: Poliana M. <pol...@gm...> - 2005-03-02 17:58:34
|
Hi Sucheta, I found in the list a message its on the LoadBlastSimFast. Your archive is: -------------------------------------------------------------------------------------------------- > 436644 (242 subjects) Sum: NP_148637.1:::149:408:927749:1330362:1:1905:108:182:0:-2 HSP1: NP_148637.1:108:182:1905:::149:408:927749:1330362:0:-2 Sum: NP_558777.1:::181:440:927740:1330359:1:1808:103:163:0:-2 --------------------------------------------------------------------------------------------------- You it substituted values as "NP_148637.1" for GusID's? Or it inserted thus exactly in the database (dots.similarity and dots.similarityspan)? Poliana |
|
From: Ed R. <ero...@ug...> - 2005-03-02 16:23:12
|
We need a definition for the new (3.5) Transmembrane Feature
View _immediately_ for the cryptodb project. All we need are
5 aliased fields in a standard dots.AAFeatureImp subclassed
view. I want to propose the following, which meets our needs.
If anyone wants to add any more aliased views to this, please
feel free to do so. If there are any problems with this,
please post those also.
-Ed
create view dots.TransMembraneAAFeature as
select aa_feature_id,
aa_sequence_id,
feature_name_id,
parent_id,
na_feature_id,
subclass_view,
sequence_ontology_id,
description,
pfam_entry_id,
motif_aa_sequence_id,
repeat_type_id,
external_database_release_id,
source_id,
prediction_algorithm_id,
is_predicted,
review_status_id,
int1 as length,
string1 as expected_aa,
string2 as first_60,
int2 as predicted_helices,
int3 as topology
from DoTS.AaFeatureImp
-----------------
Ed Robinson
Center for Tropical and Emerging Global Diseases
University of Georgia, Athens, GA 30602
ero...@ug.../(706)542.1447/254.8883
|
|
From: Steve F. <sfi...@pc...> - 2005-02-27 13:48:11
|
Jeetendra- sorry, i was on vacation. (i am posting this to gusdev) unfortunately, the plugin we use for that was written a while ago, specifically for our DoTS project. It calls CAP4 to do the assembling, and then writes the assemblies into the db. A better design would have separated the two steps (assembling and loading). If you'd like i could send you that plugin. Perhaps you could use it as a starting point. We'd be interested in a plugin that loaded assemblies, because we'll be retiring this plugin within the year probably. steve Jeetendra Soneja wrote: > > Hi Steve > > I have a set of assembly sequences that I would like to load into GUS. > GUS has Assembly and AssemblySequence tables for this. > > However, I couldn't find a plugin which does this. > > What do you think is the best way to load such data into GUS ? > > Thanks a lot, > Jeetendra. |
|
From: Sucheta T. <su...@vb...> - 2005-02-26 00:16:28
|
Folks, Do we not need to store the reviewer's information in GUS as well? Currently, we are storing it elsewhere. But I think it will be a good addition and also for authentication and verification. Thanks Sucheta |
|
From: Michael S. <msa...@pc...> - 2005-02-25 22:11:36
|
Hi Alan, This is a know Oracle bug. See this previous list posting for more information: http://sourceforge.net/mailarchive/message.php?msg_id=10486611 --Mike Alan Gingle wrote: > Hello, > > Recently a colleague brought a problem to my attention that involved the > DBD::Oracle client accessing a 10g database. He received the following > error message. > > ---------------------------------------------------------------- > > >>DBD::Oracle::st execute failed: ORA-00600: internal error >>code, arguments: [kpofdr-long], [], [], [], [], [], [], [] >>(DBD ERROR: error possibly near <*> indicator at char 19 in >>'select * from SRes.<*>TaxonName where name = :p1') [for >>Statement "select * from SRes.TaxonName where name = ?" with >>ParamValues: :p1='Trypanosoma cruzi'] at >>/var/local/GUS-Test/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm >>line 251. >>Failed executing: >> select * from SRes.TaxonName where name = ? >> >> with values 'Trypanosoma cruzi' >> errormsg: ORA-00600: internal error code, arguments: >>[kpofdr-long], [], [], [], [], [], [], [] (DBD ERROR: error >>possibly near <*> indicator at char 19 in 'select * from >>SRes.<*>TaxonName where name = :p1') >> > > > --------------------------------- > > A Google search turned up another example of this error message. > > ---------------------------------------------------------------- > > the following program: > > use strict; > use DBI; > > my $dbh = DBI->connect(qw( dbi:Oracle: T3_JLL T3_JLL ), { PrintError > => 0 }); > $dbh->do(q{DROP TABLE Person}); > $dbh->disconnect; > > $dbh = DBI->connect(qw( dbi:Oracle: T3_JLL T3_JLL ), { PrintError => > 1 }); > $dbh->do(q{CREATE TABLE Person (id INTEGER PRIMARY KEY, type > INTEGER, name VARCHAR(255))}); > $dbh->do(q{INSERT INTO Person ( id, type, name ) VALUES ( 1, 1, > 'Homer' )}); > > my $sth = $dbh->prepare('SELECT Person.name, Person.type FROM Person > WHERE Person.id = ?') or die; > $sth->execute(1); > DBI::dump_results($sth); > > .... generates an internal error: > > DBD::Oracle::st execute failed: ORA-00600: internal error code, > arguments: [kpofdr-long], [], [], [], [], [], [], [] (DBD ERROR: error > possibly near <*> indicator at char 37 in 'SELECT Person.name, Person.type > FROM <*>Person WHERE Person.id = :p1') [for Statement "SELECT Person.name, > Person.type FROM Person WHERE Person.id = ?" with ParamValues: :p1=1] at > /home/jll/t.pl line 16, <MYSELF> line 19. > DBD::Oracle::st fetch failed: ERROR no statement executing (perhaps > you need to call execute first) [for Statement "SELECT Person.name, > Person.type FROM Person WHERE Person.id = ?" with ParamValues: :p1=1] at > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi/DBI .pm line 986, > <MYSELF> line 19. > > 0 rows (-1: ERROR no statement executing (perhaps you need to call > execute first)) > > Oddly this error seems related to the presence of a primary key. If I change > the CREATE TABLE line into: > > $dbh->do(q{CREATE TABLE Person (id INTEGER, type INTEGER, name > VARCHAR(255))}); > > ....everything works as expected. Also, it works if I comment out the > INSERT. > > Has anybody seen this before? > > I use DBD::Oracle 1.16, Oracle Enterprise Manager 10g an dperl 5.8.5 on a > Fedora Core 3. > > ------------------------------------------------------------------- > > Has anyone experienced this problem and, if so, is a patch available that > will fix it? > > Thanks in advance, > > Alan > > > Alan R. Gingle (Ph.D.) > Senior Research Scientist > Center for Applied Genetic Technologies > University of Georgia > Athens, GA 30602, USA > > |
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From: Sucheta T. <su...@vb...> - 2005-02-25 20:32:10
|
Hi Poliana, You should typically use the regex which should be the subject id in the HSP section. Pl. Check the script I have sent you. There are some details about it in the comment section of the script In your case, regex will be : \S+\|(.*?)\| But caution here: There may be some issues. Even though your blast results are parsed in our machine, it may not work for you . You may need to consider the following points. 1. Pass one output at a time(I had mentioned about this earlier- for this you may need to split the blast output into individual files and then pass them through a shell script or perl script to parseblastsimilarity.pl). 2. I have again modified the BlastAnal.pm file for small parsing and space issues, so you may need to check that. So, just let me know after modifying the regex if it still did not work, then you need to tweak the BlastAnal.pm littlebit. Even after you parse, you may not be able to upload this data into dots.similarity and dots.similarityspan tables, since you need numbers in places of query_id and subject_id. These numbers are going to be referenced to suject_table and query_tables. So, in this case, you either change them to some numbers or change the plugin. HTH Sucheta Since I had this problem earlier and I had to spend lots of time solving this, I am ccing this to the group, it may help others. At 04:41 PM 2/25/2005 -0300, you wrote: >see... > >[bioinfo@kineto2 bioinfo]$ perl parseblastsimilarity.pl >--regex='(\d+)\s+\d+\s+\d+' --inputFile='new.out' >--outputFile='parse.out' --adjustMatch > >Inside analyzeblast >DEBUGGING ON >algorithm = BLASTX >ParseType='1' >algorithm = BLASTX >ParseType='1' >algorithm = BLASTX >ParseType='1' >Matching query: 390 416 >Can't call method "getID" on an undefined value at >/opt/GUS/gus_home/lib/perl/CBIL/Bio/Blast/BlastAnal.pm line 136, ><INPUT> line 5761. > >---------- > >[bioinfo@kineto2 bioinfo]$ more parse.out >Cutoff parameters: > P value: 1e-05 > Length: 10 > Percent Identity: 20 > >Cutoff parameters: > P value: 1e-05 > Length: 10 > Percent Identity: 20 > >Cutoff parameters: > P value: 1e-05 > Length: 10 > Percent Identity: 20 > >Cutoff parameters: > P value: 1e-05 > Length: 10 > Percent Identity: 20 > >Cutoff parameters: > P value: 1e-05 > Length: 10 > Percent Identity: 20 > >Cutoff parameters: > P value: 1e-05 > Length: 10 > Percent Identity: 20 >--More--(74%) > >----- > >Poliana > >On Fri, 25 Feb 2005 14:36:17 -0500, Sucheta Tripathy <su...@vb...> >wrote: > > Ok now if possible, send me the output, I will check and see if it is the > > space problem. > > > > Sucheta > > > > At 04:22 PM 2/25/2005 -0300, you wrote: > > >Hi Sucheta, > > > > > >I twirled other blast... now I have one output with "querie name". But > > >I continue with same the problems...if you it will have another > > >idea... > > > > > >Thanks > > > > > > > > >On Fri, 25 Feb 2005 11:38:46 -0500, Sucheta Tripathy <su...@vb...> > > >wrote: > > > > I think its important that your blast output should have the query > name. I > > > > did not check your fasta file, but make sure that your blast output has > > > > query name, else it will not be able to parse the output. > > > > > > > > Sucheta > > > > > > > > At 01:35 PM 2/25/2005 -0300, you wrote: > > > > >ok...in my "RESULTADO_FASTA" does not have "query name".... > > > > >But and my original file (result blast) > > > > >"leimajor-nr-poliana-blastx-01.out" also it does not have? > > > > > > > > > >Poliana > > > > > > > > > > > > > > >On Fri, 25 Feb 2005 11:26:17 -0500, Sucheta Tripathy > <su...@vb...> > > > > >wrote: > > > > > > Hi Poliana, > > > > > > > > > > > > By having a quick look at your output, it look sto me that the > > > problem lies > > > > > > with your not having a "Query name". How do you want to store it if > > > it does > > > > > > not have a query name? > > > > > > > > > > > > Sucheta > > > > > > > > > > > > At 01:16 PM 2/25/2005 -0300, you wrote: > > > > > > >sorry... but I only removed (script) the sequencias that > interest me > > > > > > >of the result of blast....and I want to insert in the GUS. The > > > > > > >original archive is this in annex. > > > > > > > > > > > > > >Poliana > > > > > > > > > > > > > > > > > > > > >On Fri, 25 Feb 2005 11:06:46 -0500, Sucheta Tripathy > > > <su...@vb...> > > > > > > >wrote: > > > > > > > > Hi Poliana, > > > > > > > > > > > > > > > > I wanted the blast output, not the sequence itself :) Can you > > > > > please snd a > > > > > > > > sample of that. > > > > > > > > > > > > > > > > Sucheta > > > > > > > > > > > > > > > > At 12:48 PM 2/25/2005 -0300, you wrote: > > > > > > > > >yes...of course!!! > > > > > > > > >it's in annex... > > > > > > > > > > > > > > > > > >Poliana > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >On Fri, 25 Feb 2005 09:39:26 -0500 (EST), Sucheta Tripathy > > > > > > > > ><su...@vb...> wrote: > > > > > > > > > > Can you pl. send me a part of your blast input file? > > > > > > > > > > > > > > > > > > > > It will make easier for me to check if the problem is with > > > > > > > BlastAnal.pm or > > > > > > > > > > not. > > > > > > > > > > > > > > > > > > > > Sucheta > > > > > > > > > > > > > > > > > > > > > Ok...Sucheta! > > > > > > > > > > > > > > > > > > > > > > My "--INPUTFILE" (blast result) does not have the GUSIDs, > > > > > because I > > > > > > > > > > > twirled blast with the NR of the web. > > > > > > > > > > > It has some problem? > > > > > > > > > > > > > > > > > > > > > > Other problem is: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------------------------------------------ > > > > > > > > > > > [bioinfo@kineto2 bioinfo]$ perl parseblastsimilarity.pl > > > > > > > > > > > --regex='(\d+)\s+\d+\s+\d+' > > > > > > > > > > > --inputFile='leimajor-nr-poliana-blastx-01.out' > > > > > > > > > > > --outputFile='parse.out' --adjustMatch > > > > > > > > > > > Inside analyzeblast > > > > > > > > > > > DEBUGGING ON > > > > > > > > > > > algorithm = BLASTX > > > > > > > > > > > ParseType='1' > > > > > > > > > > > algorithm = BLASTX > > > > > > > > > > > ParseType='1' > > > > > > > > > > > algorithm = BLASTX > > > > > > > > > > > ParseType='1' > > > > > > > > > > > Matching query: 821 847 > > > > > > > > > > > Can't call method "getID" on an undefined value at > > > > > > > > > > > /opt/GUS/gus_home/lib/perl/CBIL/Bio/Blast/BlastAnal.pm > > > line 136, > > > > > > > > > > > <INPUT> line 5599. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > --------------------------------------------------------------------------------------------------------------------------- > > > > > > > > > > > I read that the function "getID" catches the primary key > > > in the > > > > > > > > > > > Oracle, but I am using PostgreSQL. > > > > > > > > > > > ?? > > > > > > > > > > > > > > > > > > > > > > Poliana > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Fri, 25 Feb 2005 09:04:12 -0500 (EST), Sucheta > Tripathy > > > > > > > > > > > <su...@vb...> wrote: > > > > > > > > > > >> Hi Poliana, > > > > > > > > > > >> > > > > > > > > > > >> This could be happening because of 2 reasons. One > may be the > > > > > > > regex that > > > > > > > > > > >> you are providing is not right. The other could be in > > > > > > > BlastAnal.pm. Just > > > > > > > > > > >> go there and see(at some point I have changed my > > > version, it is > > > > > > > to do > > > > > > > > > > >> with > > > > > > > > > > >> a space i.e; in original version it is \s, but I changed > > > it to > > > > > > > \s+. If > > > > > > > > > > >> you > > > > > > > > > > >> did not find it, I will tell you after sometime, > once I am > > > > > back at > > > > > > > > > > >> office. > > > > > > > > > > >> > > > > > > > > > > >> Ok > > > > > > > > > > >> > > > > > > > > > > >> Sucheta > > > > > > > > > > >> > > > > > > > > > > >> > Hi Sucheta, > > > > > > > > > > >> > > > > > > > > > > > >> > I am trying to twirl script "parseblastsimilarity.pl" > > > > > > > again....but I > > > > > > > > > > >> > am catching the following result: > > > > > > > > > > >> > > > > > > > > > > > >> > [bioinfo@kineto2 bioinfo]$ perl > parseblastsimilarity.pl > > > > > > > > > > >> > --regex='(\d+)\s+\d+\s+\d+' > --inputFile='RESULTADO_FASTA' > > > > > > > > > > >> > --outputFile='parse.out' --adjustMatch > > > > > > > > > > >> > > > > > > > > > > > >> > Inside analyzeblast > > > > > > > > > > >> > DEBUGGING ON > > > > > > > > > > >> > > > > > > > > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------------------------------------------- > > > > > > > > > > >> > > > > > > > > > > > >> > [bioinfo@kineto2 bioinfo]$ more parse.out > > > > > > > > > > >> > Cutoff parameters: > > > > > > > > > > >> > P value: 1e-05 > > > > > > > > > > >> > Length: > > > > > > > > > > >> > 10 > > > > > > > > > > >> > Percent Identity: 20 > > > > > > > > > > >> > > > > > > > > > > > >> >> (0 subjects) > > > > > > > > > > >> > > > > > > > > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------------------------------------------- > > > > > > > > > > >> > > > > > > > > > > > >> > I believe that this is not the certain waited... > > > > > > > > > > >> > ??? > > > > > > > > > > >> > > > > > > > > > > > >> > []'s > > > > > > > > > > >> > Poliana > > > > > > > > > > >> > > > > > > > > > > > >> > > > > > > > > > > >> -- > > > > > > > > > > >> Sucheta Tripathy > > > > > > > > > > >> Virginia Bioinformatics Institute Phase-I > > > > > > > > > > >> Washington street. > > > > > > > > > > >> Virginia Tech. > > > > > > > > > > >> Blacksburg,VA 24061-0447 > > > > > > > > > > >> phone:(540)231-8138 > > > > > > > > > > >> Fax: (540) 231-2606 > > > > > > > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > Sucheta Tripathy > > > > > > > > > > Virginia Bioinformatics Institute Phase-I > > > > > > > > > > Washington street. > > > > > > > > > > Virginia Tech. > > > > > > > > > > Blacksburg,VA 24061-0447 > > > > > > > > > > phone:(540)231-8138 > > > > > > > > > > Fax: (540) 231-2606 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > |
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From: Poliana M. <pol...@gm...> - 2005-02-24 15:43:08
|
Thanks... When that to finish I sending the result! Poliana On Thu, 24 Feb 2005 10:23:03 -0500, John Iodice <io...@pc...> wrote: > Poliana, > > I ran LoadNRDB a couple of weeks ago, and it did take about a day to > load all of NRDB. So don't worry about that. Do check out the final > output when it finishes; if you see anything amiss there, post to the > group or email me or Debbie. > > John > > On Thu, 2005-02-24 at 06:08, Poliana Mateus wrote: > > Hi Debbie > > > > Yesterday I started to load the LoadNRDB and still no finished. This normal? > > > > It sees output: > > > > Wed Feb 23 13:17:46 2005 ***COMMIT ON*** > > > > There are 15 entries in the source database hash > > Wed Feb 23 14:06:52 2005 There are 5821294 gi to taxon_id pairs > > > > Wed Feb 23 14:11:53 2005 1000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:12:16 2005 2000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:12:40 2005 3000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:13:07 2005 4000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:13:51 2005 6000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:14:37 2005 8000 sets have been processed > > and put in the NRDBTemp table > > > > Wed Feb 23 14:15:23 2005 10000 sets have been processed > > and put in the NRDBTemp table > > > > > > ........ > > > > Poliana > > > > > > On Wed, 23 Feb 2005 10:42:31 -0500, Deborah Pinney > > <pi...@pc...> wrote: > > > I believe you are missing a couple ext_db_rel_ids for the source > > > databases in the nr file. This is the string I use. Of course the > > > release_ids are specific to our database. > > > > > > 7475:gb,7476:emb,7477:dbj,7478:pir,7479:prf,7480:sp,7481:pdb,7514:pat,7515:bbs,7516:gnl,7474:ref,7517:lcl,7482:genpept,7483:tpe,8034:tpd > > > > > > also, extDbRelId is an int, not a string > > > > > > Debbie > > > > > > > > > Poliana Mateus wrote: > > > > > > >I am trying to run the LoadNRD, but I have the following error: > > > > > > > >[poliana@phytomonas gus_home]$ ga GUS::Common::Plugin::LoadNRDB > > > >--algoinvo=1 --comment="Loading NRDB data" --temp_login="gus" > > > >--sourceDB="93:ref,102:emb,156:gb,118:pir,119:sp,148:dbj,144:prf,48:pdb,46:pat,58:bbs,173:lcl,71:gnl" > > > >--temp_password="******" --dbi_str="dbi:Pg:dbname=tryps" > > > >--gitax="/usr/local/db/local/nrdb/gi_taxid_prot.dmp" > > > >--nrdb="/usr/local/db/local/nrdb/nr" --extDbRelId="3027" --maketemp > > > >--plugin --delete --commit > > > > > > > >Wed Feb 23 09:25:04 2005 ***COMMIT ON*** > > > > > > > >There are 12 entries in the source database hash > > > >Wed Feb 23 10:25:20 2005 There are 5821294 gi to taxon_id pairs > > > > > > > >Wed Feb 23 10:30:27 2005 1000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >Wed Feb 23 10:31:20 2005 2000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >DBD::Pg::st execute failed: ERROR: null value in column > > > >"external_db_rel_id" violates not-null constraint at > > > >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line > > > >281, <NRDB> line 6374. > > > > > > > >Wed Feb 23 10:31:47 2005 3000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >Wed Feb 23 10:32:10 2005 4000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >Wed Feb 23 10:33:15 2005 6000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >DBD::Pg::st execute failed: ERROR: null value in column > > > >"external_db_rel_id" violates not-null constraint at > > > >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line > > > >281, <NRDB> line 19995. > > > > > > > >DBD::Pg::st execute failed: ERROR: null value in column > > > >"external_db_rel_id" violates not-null constraint at > > > >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line > > > >281, <NRDB> line 20179. > > > >Wed Feb 23 10:34:03 2005 8000 sets have been processed > > > > and put in the NRDBTemp table > > > > > > > >...... > > > > > > > >-------------------------------------------------------------------------------------------------------------- > > > > > > > >somebody has idea of as to correct? > > > > > > > >Poliana > > > > > > > > > > > >------------------------------------------------------- > > > >SF email is sponsored by - The IT Product Guide > > > >Read honest & candid reviews on hundreds of IT Products from real users. > > > >Discover which products truly live up to the hype. Start reading now. > > > >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > > > >_______________________________________________ > > > >Gusdev-gusdev mailing list > > > >Gus...@li... > > > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------- > > SF email is sponsored by - The IT Product Guide > > Read honest & candid reviews on hundreds of IT Products from real users. > > Discover which products truly live up to the hype. Start reading now. > > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > -- > John Iodice > Bioinformatics Software Engineer > Computational Biology and Informatics Lab > University of Pennsylvania > http://cbil.upenn.edu > > |
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From: Poliana M. <pol...@gm...> - 2005-02-24 11:08:23
|
Hi Debbie
Yesterday I started to load the LoadNRDB and still no finished. This normal?
It sees output:
Wed Feb 23 13:17:46 2005 ***COMMIT ON***
There are 15 entries in the source database hash
Wed Feb 23 14:06:52 2005 There are 5821294 gi to taxon_id pairs
Wed Feb 23 14:11:53 2005 1000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:12:16 2005 2000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:12:40 2005 3000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:13:07 2005 4000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:13:51 2005 6000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:14:37 2005 8000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 14:15:23 2005 10000 sets have been processed
and put in the NRDBTemp table
........
Poliana
On Wed, 23 Feb 2005 10:42:31 -0500, Deborah Pinney
<pi...@pc...> wrote:
> I believe you are missing a couple ext_db_rel_ids for the source
> databases in the nr file. This is the string I use. Of course the
> release_ids are specific to our database.
>
> 7475:gb,7476:emb,7477:dbj,7478:pir,7479:prf,7480:sp,7481:pdb,7514:pat,7515:bbs,7516:gnl,7474:ref,7517:lcl,7482:genpept,7483:tpe,8034:tpd
>
> also, extDbRelId is an int, not a string
>
> Debbie
>
>
> Poliana Mateus wrote:
>
> >I am trying to run the LoadNRD, but I have the following error:
> >
> >[poliana@phytomonas gus_home]$ ga GUS::Common::Plugin::LoadNRDB
> >--algoinvo=1 --comment="Loading NRDB data" --temp_login="gus"
> >--sourceDB="93:ref,102:emb,156:gb,118:pir,119:sp,148:dbj,144:prf,48:pdb,46:pat,58:bbs,173:lcl,71:gnl"
> >--temp_password="******" --dbi_str="dbi:Pg:dbname=tryps"
> >--gitax="/usr/local/db/local/nrdb/gi_taxid_prot.dmp"
> >--nrdb="/usr/local/db/local/nrdb/nr" --extDbRelId="3027" --maketemp
> >--plugin --delete --commit
> >
> >Wed Feb 23 09:25:04 2005 ***COMMIT ON***
> >
> >There are 12 entries in the source database hash
> >Wed Feb 23 10:25:20 2005 There are 5821294 gi to taxon_id pairs
> >
> >Wed Feb 23 10:30:27 2005 1000 sets have been processed
> > and put in the NRDBTemp table
> >
> >Wed Feb 23 10:31:20 2005 2000 sets have been processed
> > and put in the NRDBTemp table
> >
> >DBD::Pg::st execute failed: ERROR: null value in column
> >"external_db_rel_id" violates not-null constraint at
> >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
> >281, <NRDB> line 6374.
> >
> >Wed Feb 23 10:31:47 2005 3000 sets have been processed
> > and put in the NRDBTemp table
> >
> >Wed Feb 23 10:32:10 2005 4000 sets have been processed
> > and put in the NRDBTemp table
> >
> >Wed Feb 23 10:33:15 2005 6000 sets have been processed
> > and put in the NRDBTemp table
> >
> >DBD::Pg::st execute failed: ERROR: null value in column
> >"external_db_rel_id" violates not-null constraint at
> >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
> >281, <NRDB> line 19995.
> >
> >DBD::Pg::st execute failed: ERROR: null value in column
> >"external_db_rel_id" violates not-null constraint at
> >/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
> >281, <NRDB> line 20179.
> >Wed Feb 23 10:34:03 2005 8000 sets have been processed
> > and put in the NRDBTemp table
> >
> >......
> >
> >--------------------------------------------------------------------------------------------------------------
> >
> >somebody has idea of as to correct?
> >
> >Poliana
> >
> >
> >-------------------------------------------------------
> >SF email is sponsored by - The IT Product Guide
> >Read honest & candid reviews on hundreds of IT Products from real users.
> >Discover which products truly live up to the hype. Start reading now.
> >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
> >_______________________________________________
> >Gusdev-gusdev mailing list
> >Gus...@li...
> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> >
>
>
|
|
From: Sucheta T. <su...@vb...> - 2005-02-23 15:40:25
|
Hi Mike, Thanks for the tips. In fact here at VBI, we have the DBA team helping us out in checking the performance issues, and after doing some research Sally(one of our DBA) informed me that the large dataset may be the cause of this. Probably one option left for us is to have materialized views on these tables. Sucheta At 10:33 AM 2/23/2005 -0500, Michael Saffitz wrote: >Hi Sucheta, > >A few general query optimization points: > >1) It's best to start by looking at the query execution plan, to determine >what exactly is going on. In Oracle, you'll need to create the necessary >plan table, and then use the explain plan for... command. Refer to >Oracle's documentation for details. > >2) The plan may reveal some ways in which you can speed up the query. For >example, if the query is resulting in several full table scans of very >large tables, it's very likely that an index on the affected columns will >improve performance. > >3) If the plan looks acceptable, but the query is still slow, then you may >need to dig deeper. If it's purely an issue of a complex query over a >large amount of data, then a materialized view may help (if the query is >run frequently). Otherwise, you may need to examine where the bottleneck >is coming from-- is it cpu, disk, or something else (i.e. such as other >user's use of the system)? > >Ultimately, sometimes a query is just slow. Our similarity table is many, >many gigabytes (I believe upwards of 30), and any complex query on that >amount of data is going to be slow-- there's only so much optimization >that can occur. > >Hope this helps, > >Mike > > >Sucheta Tripathy wrote: >>Folks, >>I don't know if any of you encountered this problem, but for us, it has >>been a major bottleneck to query the similarity and similarityspan tables >>to get the desirable output. >>For example if I say a query: >>$sql="select /*+CHOOSE*/ distinct ss.query_start, >>ss.query_end,ss.is_reversed >>,ss.reading_frame,s.subject_id, to_char(s.pvalue_mant,'FM9990.099') || >>'e' || TO >>_CHAR(s.pvalue_exp,'FMS999'), eaa.name, s.similarity_id from >>dots.similarity s >>, dots.similarityspan ss, dots.transcript t, dots.externalaasequence >>eaa where >>t.na_feature_id=464205 and t.gene=to_char(s.query_id) and >>s.similarity_id=ss.sim >>ilarity_id and s.subject_id=eaa.source_id and rownum < 10 order by >>s.similarity_ >>id"; >>It takes atleast 5 minutes. One thing to note here is here for the >>transcript corresponding to the na_feature_id is blasted against only one >>database, so the query is quite straight forward. But there are instances >>where the scaffolds are blasted aganst 23 different organisms. In that >>case, in order to obtain the value against one particular database, I use >>much nested query going and getting the value from externaldatabase and >>externaldatabaserelease and then using it in similarity table. >>I was wondering if anyone has any efficient way of querying these tables. >>Thanks >>Sucheta >> >>------------------------------------------------------- >>SF email is sponsored by - The IT Product Guide >>Read honest & candid reviews on hundreds of IT Products from real users. >>Discover which products truly live up to the hype. Start reading now. >>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Angel P. <an...@ma...> - 2005-02-23 15:40:10
|
Sucheta, It is always a good idea to include an the output of "EXPLAIN PLAN" when asking how to optimize queries. Usually well-placed indexes will take care of long running queries. *EXPLAIN PLAN* [*SET STATEMENT_ID* = 'text'] [*INTO* [schema .] table [@ dblink]] *FOR* statement; Output defaults to a plan table in your schema, unless you give it a plan table to insert into. Oracle has a script for creating this table, |UTLXPLAN.SQL| Attached is a SQL script to output the results from the plan table. Postgres must have some similar functionality. Angel Sucheta Tripathy wrote: > Folks, > > I don't know if any of you encountered this problem, but for us, it > has been a major bottleneck to query the similarity and similarityspan > tables to get the desirable output. > > For example if I say a query: > > $sql="select /*+CHOOSE*/ distinct ss.query_start, > ss.query_end,ss.is_reversed > ,ss.reading_frame,s.subject_id, to_char(s.pvalue_mant,'FM9990.099') || > 'e' || TO > _CHAR(s.pvalue_exp,'FMS999'), eaa.name, s.similarity_id from > dots.similarity s > , dots.similarityspan ss, dots.transcript t, dots.externalaasequence > eaa where > t.na_feature_id=464205 and t.gene=to_char(s.query_id) and > s.similarity_id=ss.sim > ilarity_id and s.subject_id=eaa.source_id and rownum < 10 order by > s.similarity_ > id"; > > It takes atleast 5 minutes. One thing to note here is here for the > transcript corresponding to the na_feature_id is blasted against only > one database, so the query is quite straight forward. But there are > instances where the scaffolds are blasted aganst 23 different > organisms. In that case, in order to obtain the value against one > particular database, I use much nested query going and getting the > value from externaldatabase and externaldatabaserelease and then using > it in similarity table. > > I was wondering if anyone has any efficient way of querying these tables. > > Thanks > > Sucheta > > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide > Read honest & candid reviews on hundreds of IT Products from real users. > Discover which products truly live up to the hype. Start reading now. > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 |
|
From: Deborah P. <pi...@pc...> - 2005-02-23 15:38:04
|
I believe you are missing a couple ext_db_rel_ids for the source
databases in the nr file. This is the string I use. Of course the
release_ids are specific to our database.
7475:gb,7476:emb,7477:dbj,7478:pir,7479:prf,7480:sp,7481:pdb,7514:pat,7515:bbs,7516:gnl,7474:ref,7517:lcl,7482:genpept,7483:tpe,8034:tpd
also, extDbRelId is an int, not a string
Debbie
Poliana Mateus wrote:
>I am trying to run the LoadNRD, but I have the following error:
>
>[poliana@phytomonas gus_home]$ ga GUS::Common::Plugin::LoadNRDB
>--algoinvo=1 --comment="Loading NRDB data" --temp_login="gus"
>--sourceDB="93:ref,102:emb,156:gb,118:pir,119:sp,148:dbj,144:prf,48:pdb,46:pat,58:bbs,173:lcl,71:gnl"
>--temp_password="******" --dbi_str="dbi:Pg:dbname=tryps"
>--gitax="/usr/local/db/local/nrdb/gi_taxid_prot.dmp"
>--nrdb="/usr/local/db/local/nrdb/nr" --extDbRelId="3027" --maketemp
>--plugin --delete --commit
>
>Wed Feb 23 09:25:04 2005 ***COMMIT ON***
>
>There are 12 entries in the source database hash
>Wed Feb 23 10:25:20 2005 There are 5821294 gi to taxon_id pairs
>
>Wed Feb 23 10:30:27 2005 1000 sets have been processed
> and put in the NRDBTemp table
>
>Wed Feb 23 10:31:20 2005 2000 sets have been processed
> and put in the NRDBTemp table
>
>DBD::Pg::st execute failed: ERROR: null value in column
>"external_db_rel_id" violates not-null constraint at
>/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
>281, <NRDB> line 6374.
>
>Wed Feb 23 10:31:47 2005 3000 sets have been processed
> and put in the NRDBTemp table
>
>Wed Feb 23 10:32:10 2005 4000 sets have been processed
> and put in the NRDBTemp table
>
>Wed Feb 23 10:33:15 2005 6000 sets have been processed
> and put in the NRDBTemp table
>
>DBD::Pg::st execute failed: ERROR: null value in column
>"external_db_rel_id" violates not-null constraint at
>/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
>281, <NRDB> line 19995.
>
>DBD::Pg::st execute failed: ERROR: null value in column
>"external_db_rel_id" violates not-null constraint at
>/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
>281, <NRDB> line 20179.
>Wed Feb 23 10:34:03 2005 8000 sets have been processed
> and put in the NRDBTemp table
>
>......
>
>--------------------------------------------------------------------------------------------------------------
>
>somebody has idea of as to correct?
>
>Poliana
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now.
>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
|
|
From: Michael S. <msa...@pc...> - 2005-02-23 15:33:57
|
Hi Sucheta, A few general query optimization points: 1) It's best to start by looking at the query execution plan, to determine what exactly is going on. In Oracle, you'll need to create the necessary plan table, and then use the explain plan for... command. Refer to Oracle's documentation for details. 2) The plan may reveal some ways in which you can speed up the query. For example, if the query is resulting in several full table scans of very large tables, it's very likely that an index on the affected columns will improve performance. 3) If the plan looks acceptable, but the query is still slow, then you may need to dig deeper. If it's purely an issue of a complex query over a large amount of data, then a materialized view may help (if the query is run frequently). Otherwise, you may need to examine where the bottleneck is coming from-- is it cpu, disk, or something else (i.e. such as other user's use of the system)? Ultimately, sometimes a query is just slow. Our similarity table is many, many gigabytes (I believe upwards of 30), and any complex query on that amount of data is going to be slow-- there's only so much optimization that can occur. Hope this helps, Mike Sucheta Tripathy wrote: > Folks, > > I don't know if any of you encountered this problem, but for us, it has > been a major bottleneck to query the similarity and similarityspan > tables to get the desirable output. > > For example if I say a query: > > $sql="select /*+CHOOSE*/ distinct ss.query_start, > ss.query_end,ss.is_reversed > ,ss.reading_frame,s.subject_id, to_char(s.pvalue_mant,'FM9990.099') || > 'e' || TO > _CHAR(s.pvalue_exp,'FMS999'), eaa.name, s.similarity_id from > dots.similarity s > , dots.similarityspan ss, dots.transcript t, dots.externalaasequence > eaa where > t.na_feature_id=464205 and t.gene=to_char(s.query_id) and > s.similarity_id=ss.sim > ilarity_id and s.subject_id=eaa.source_id and rownum < 10 order by > s.similarity_ > id"; > > It takes atleast 5 minutes. One thing to note here is here for the > transcript corresponding to the na_feature_id is blasted against only > one database, so the query is quite straight forward. But there are > instances where the scaffolds are blasted aganst 23 different organisms. > In that case, in order to obtain the value against one particular > database, I use much nested query going and getting the value from > externaldatabase and externaldatabaserelease and then using it in > similarity table. > > I was wondering if anyone has any efficient way of querying these tables. > > Thanks > > Sucheta > > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide > Read honest & candid reviews on hundreds of IT Products from real users. > Discover which products truly live up to the hype. Start reading now. > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: Sucheta T. <su...@vb...> - 2005-02-23 15:23:10
|
Folks, I don't know if any of you encountered this problem, but for us, it has been a major bottleneck to query the similarity and similarityspan tables to get the desirable output. For example if I say a query: $sql="select /*+CHOOSE*/ distinct ss.query_start, ss.query_end,ss.is_reversed ,ss.reading_frame,s.subject_id, to_char(s.pvalue_mant,'FM9990.099') || 'e' || TO _CHAR(s.pvalue_exp,'FMS999'), eaa.name, s.similarity_id from dots.similarity s , dots.similarityspan ss, dots.transcript t, dots.externalaasequence eaa where t.na_feature_id=464205 and t.gene=to_char(s.query_id) and s.similarity_id=ss.sim ilarity_id and s.subject_id=eaa.source_id and rownum < 10 order by s.similarity_ id"; It takes atleast 5 minutes. One thing to note here is here for the transcript corresponding to the na_feature_id is blasted against only one database, so the query is quite straight forward. But there are instances where the scaffolds are blasted aganst 23 different organisms. In that case, in order to obtain the value against one particular database, I use much nested query going and getting the value from externaldatabase and externaldatabaserelease and then using it in similarity table. I was wondering if anyone has any efficient way of querying these tables. Thanks Sucheta |
|
From: Poliana M. <pol...@gm...> - 2005-02-23 13:49:39
|
I am trying to run the LoadNRD, but I have the following error:
[poliana@phytomonas gus_home]$ ga GUS::Common::Plugin::LoadNRDB
--algoinvo=1 --comment="Loading NRDB data" --temp_login="gus"
--sourceDB="93:ref,102:emb,156:gb,118:pir,119:sp,148:dbj,144:prf,48:pdb,46:pat,58:bbs,173:lcl,71:gnl"
--temp_password="******" --dbi_str="dbi:Pg:dbname=tryps"
--gitax="/usr/local/db/local/nrdb/gi_taxid_prot.dmp"
--nrdb="/usr/local/db/local/nrdb/nr" --extDbRelId="3027" --maketemp
--plugin --delete --commit
Wed Feb 23 09:25:04 2005 ***COMMIT ON***
There are 12 entries in the source database hash
Wed Feb 23 10:25:20 2005 There are 5821294 gi to taxon_id pairs
Wed Feb 23 10:30:27 2005 1000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 10:31:20 2005 2000 sets have been processed
and put in the NRDBTemp table
DBD::Pg::st execute failed: ERROR: null value in column
"external_db_rel_id" violates not-null constraint at
/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
281, <NRDB> line 6374.
Wed Feb 23 10:31:47 2005 3000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 10:32:10 2005 4000 sets have been processed
and put in the NRDBTemp table
Wed Feb 23 10:33:15 2005 6000 sets have been processed
and put in the NRDBTemp table
DBD::Pg::st execute failed: ERROR: null value in column
"external_db_rel_id" violates not-null constraint at
/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
281, <NRDB> line 19995.
DBD::Pg::st execute failed: ERROR: null value in column
"external_db_rel_id" violates not-null constraint at
/usr/local/GUS/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line
281, <NRDB> line 20179.
Wed Feb 23 10:34:03 2005 8000 sets have been processed
and put in the NRDBTemp table
......
--------------------------------------------------------------------------------------------------------------
somebody has idea of as to correct?
Poliana
|
|
From: <fed...@bi...> - 2005-02-21 17:32:45
|
Yes, of course... It's why I don't understand where I have to move it! > In your directory /usr/local/src/gus-related/ontology/ exist the file > "component.ontology"?? > > Poliana > > > On Mon, 21 Feb 2005 18:18:53 +0100 (CET), fed...@bi... > <fed...@bi...> wrote: >> Thanks Poliana! >> For LoadTaxon it's ok!!! >> For GoOntology I always have the same error: >> >> ga GUS::GOPredict::Plugin::LoadGoOntology \ >> > --file_path=/usr/local/src/gus-related/ontology/ \ >> > --process_db_id=3003 \ >> > --process_ext_db_rel=6 \ >> > --function_db_id=3001 \ >> > --function_ext_db_rel=33 \ >> > --component_db_id=3002 \ >> > --component_ext_db_rel=28 \ >> > --create_release >> /usr/local/src/gus-related/ontology/Mon Feb 21 18:02:13 2005 loading >> all .ontology files in /usr/local/src/gus-related/ontology/ in >> preparation >> for parsing >> Note: did not find file component.ontology in directory >> CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2380)->getPath. >> To load this branch of the ontology specified by component.ontology, >> please put that file in the directory. >> Note: did not find file process.ontology in directory >> CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2380)->getPath. >> To load this branch of the ontology specified by process.ontology, >> please put that file in the directory. >> Note: did not find file function.ontology in directory >> CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2380)->getPath. >> To load this branch of the ontology specified by function.ontology, >> please put that file in the directory. >> Mon Feb 21 18:02:13 2005 parsing all .ontology files in >> preparation >> for inserting into database >> Mon Feb 21 18:02:13 2005 parsing finished; loading ontology into >> database >> Mon Feb 21 18:02:13 2005 RESULT Created 0 entries in GOTerm, 0 >> entries in GORelationship, and 0 entries in GOSynonym. Skipped 0 total >> entries >> >> I understand it's a problem releted with che *.ontology path, but I >> really >> don't know where I have to put my files! I think it suggests the path >> ..../CBIL/Bio/GeneOntologyParser: I put there my files but nothing >> changed! >> Do you understand something more? >> Cheers >> Federica >> >> >> > Hi Federica, >> > >> > I run thus: >> > >> > GoOntology: >> > >> > ga GUS::GOPredict::Plugin::LoadGoOntology >> > --file_path=/usr/local/db/local/ontology/ --process_db_id=3003 >> > --process_ext_db_rel=6 --function_db_id=3001 --function_ext_db_rel=33 >> > --component_db_id=3002 ââ¬"component_ext_db_rel=28 --create_release >> > >> > See if your files (*.ontology) are in the correct path. >> > >> > *************************************************************************************************** >> > >> > LoadTaxon: >> > >> > ga GUS::Common::Plugin::LoadTaxon >> > -gencode=/usr/local/db/local/taxonomy/gencode.dmp >> > --names=/usr/local/db/local/taxonomy/names.dmp >> > --nodes=/usr/local/db/local/taxonomy/nodes.dmp >> > --merged=/usr/local/db/local/taxonomy/merged.dmp >> > >> > >> > Change for its your path.... >> > >> > Poliana >> > >> > >> > On Mon, 21 Feb 2005 16:37:22 +0100 (CET), fed...@bi... >> > <fed...@bi...> wrote: >> >> Thanks, but I've downloaded from there, and I also have right >> >> privileges...! >> >> I tried also to include merged.dmp even if it's not named in the >> >> bootstrap >> >> instructions!! But nothing good happened! >> >> Any other suggestions? >> >> Federica >> >> >> >> >> >> > For LoadTaxon, you need to supply the names with path for all for >> >> file, >> >> > gencode.dmp,name.dmp,nodes.dump,merged.dmp. These files are >> downloaded >> >> > from NCBI (ftp://ftp.ncbi.nih.gov/pub/taxonomy) as a tarball, >> >> > taxdump.tar.Z or taxdump.tar.gz and uncompressed. >> >> > >> >> > >> >> > Debbie >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > fed...@bi... wrote: >> >> > >> >> >>Hi everybody! >> >> >>I'm here again! I'm inserting data following the bootstrap but I >> had >> >> this >> >> >>errors: >> >> >>1) for Taxonomy >> >> >>$ ga GUS::Common::Plugin::LoadTaxon \ >> >> >> >> >> >> >> >> >>>--gencode=/usr/local/src/gus_related/taxonomy/gencode.dmp \ >> >> >>>--names=/usr/local/src/gus_related/taxonomy/names.dmp \ >> >> >>>--nodes=/usr/local/src/gus_related/taxonomy/nodes.dmp >> >> >>> >> >> >>> >> >> >>ERROR: The names of the names.dmp, nodes.dmp, gencode.dmp and >> >> merged.dmp >> >> >>files must >> >> >>be provided on the command line. >> >> >>2) for GO Ontology >> >> >>$ ga GUS::GOPredict::Plugin::LoadGoOntology >> >> >>--file_path=/usr/local/src/gus-related/ontology/ \ >> >> >> >> >> >> >> >> >>>--process_db_id=3003 \ >> >> >>>--process_ext_db_rel=165 \ >> >> >>>--function_db_id=3001 \ >> >> >>>--function_ext_db_rel=164 \ >> >> >>>--component_db_id=3002 \ >> >> >>>--component_ext_db_rel=166 \ >> >> >>> >> >> >>> >> >> >> >> >> >>/usr/local/src/gus-related/ontology/Mon Feb 21 15:45:51 2005 >> >> loading >> >> >> all >> >> >>.ontology files in /usr/local/src/gus-related/ontology/ in >> preparation >> >> >> for >> >> >>parsing >> >> >>Note: did not find file component.ontology in directory >> >> >>CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. >> >> >> To load this branch of the ontology specified by >> component.ontology, >> >> >> please put that file in the directory. >> >> >>Note: did not find file process.ontology in directory >> >> >>CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. >> >> >> To load this branch of the ontology specified by process.ontology, >> >> >> please put that file in the directory. >> >> >>Note: did not find file function.ontology in directory >> >> >>CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. >> >> >> To load this branch of the ontology specified by >> function.ontology, >> >> >> please put that file in the directory. >> >> >>Mon Feb 21 15:45:51 2005 parsing all .ontology files in >> >> >> preparation >> >> >>for >> >> >>inserting into database >> >> >>Mon Feb 21 15:45:51 2005 parsing finished; loading ontology >> >> into >> >> >>database >> >> >>Mon Feb 21 15:45:51 2005 RESULT Created 0 entries in >> GOTerm, 0 >> >> >>entries in >> >> >>GORelationship, and 0 entries in GOSynonym. Skipped 0 total >> entries >> >> >> >> >> >>Any help? >> >> >>Cheers, >> >> >>Federica >> >> >> >> >> >> >> >> >> >> >> >>------------------------------------------------------- >> >> >>SF email is sponsored by - The IT Product Guide >> >> >>Read honest & candid reviews on hundreds of IT Products from real >> >> users. >> >> >>Discover which products truly live up to the hype. Start reading >> now. >> >> >>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >> >> >>_______________________________________________ >> >> >>Gusdev-gusdev mailing list >> >> >>Gus...@li... >> >> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> >> >> >> >> > >> >> > >> >> >> >> ------------------------------------------------------- >> >> SF email is sponsored by - The IT Product Guide >> >> Read honest & candid reviews on hundreds of IT Products from real >> users. >> >> Discover which products truly live up to the hype. Start reading now. >> >> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >> >> _______________________________________________ >> >> Gusdev-gusdev mailing list >> >> Gus...@li... >> >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> > >> >> > |
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